Open Access
Bioinformatics, volume 29, issue 6, pages 742-748
Improving the reuse of computational models through version control
Dagmar Waltemath
,
Ron Henkel
,
R Halke
,
Martin Scharm
,
Olaf Wolkenhauer
Publication type: Journal Article
Publication date: 2013-01-18
Journal:
Bioinformatics
scimago Q1
SJR: 2.574
CiteScore: 11.2
Impact factor: 4.4
ISSN: 13674803, 13674811, 14602059
PubMed ID:
23335018
Biochemistry
Computer Science Applications
Molecular Biology
Statistics and Probability
Computational Mathematics
Computational Theory and Mathematics
Abstract
Only models that are accessible to researchers can be reused. As computational models evolve over time, a number of different but related versions of a model exist. Consequently, tools are required to manage not only well-curated models but also their associated versions.In this work, we discuss conceptual requirements for model version control. Focusing on XML formats such as Systems Biology Markup Language and CellML, we present methods for the identification and explanation of differences and for the justification of changes between model versions. In consequence, researchers can reflect on these changes, which in turn have considerable value for the development of new models. The implementation of model version control will therefore foster the exploration of published models and increase their reusability.
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